3BEB

Crystal structure of E. coli penicillin-binding protein 5 in complex with a peptide-mimetic penicillin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18294100mM Tris pH 8.0, 8% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.5151.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.2α = 90
b = 50.4β = 120.8
c = 84.7γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2004-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
124794.30.1076.82.52543323.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0785.90.30522.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1NZO2472543325433127994.30.2380.2350.296RANDOM28.01
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.51-0.580.14-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.898
r_dihedral_angle_4_deg16.675
r_dihedral_angle_3_deg16.302
r_dihedral_angle_1_deg5.979
r_scangle_it2.287
r_scbond_it1.562
r_angle_refined_deg1.395
r_mcangle_it1.113
r_mcbond_it0.68
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.898
r_dihedral_angle_4_deg16.675
r_dihedral_angle_3_deg16.302
r_dihedral_angle_1_deg5.979
r_scangle_it2.287
r_scbond_it1.562
r_angle_refined_deg1.395
r_mcangle_it1.113
r_mcbond_it0.68
r_nbtor_refined0.302
r_nbd_refined0.204
r_xyhbond_nbd_refined0.188
r_symmetry_hbond_refined0.171
r_symmetry_vdw_refined0.17
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2732
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling